appli/CTBronchi/MoriLabelling.h

   1 // =========================================================================
   2 // @author Leonardo Florez Valencia
   3 // @email florez-l@javeriana.edu.co
   4 // =========================================================================
   5 #ifndef __CTBronchi__MoriLabelling__h__
   6 #define __CTBronchi__MoriLabelling__h__
   7
   8 #include <itkLabelStatisticsImageFilter.h>
   9 #include <fpa/Filters/BaseMarksInterface.h>
  10 #include <fpa/Filters/Image/SeedsFromLabelsInterface.h>
  11 #include <fpa/Filters/Image/DefaultTraits.h>
  12 #include <fpa/Filters/Image/RegionGrow.h>
  13 #include <fpa/Functors/RegionGrow/BinaryThreshold.h>
  14
  15 namespace CTBronchi
  16 {
  17   /**
  18    */
  19   template< class _TImage, class _TLabels >
  20   class MoriLabellingTraits
  21     : public fpa::Filters::Image::DefaultTraits< _TImage, _TLabels, typename _TLabels::PixelType >
  22   {
  23   public:
  24     typedef fpa::Filters::Image::DefaultTraits< _TImage, _TLabels, typename _TLabels::PixelType > Superclass;
  25     typedef typename Superclass::TInternalTraits  TInternalTraits;
  26     typedef typename Superclass::TMarksImage      TMarksImage;
  27     typedef typename Superclass::TFilterInterface TFilterInterface;
  28
  29     typedef fpa::Filters::BaseMarksInterface< TInternalTraits >  TMarksInterface;
  30     typedef fpa::Filters::Image::SeedsFromLabelsInterface< TInternalTraits > TSeedsInterface;
  31   };
  32
  33   /**
  34    */
  35   template< class _TImage, class _TLabels, class _TScalarImage >
  36   class MoriLabelling
  37     : public fpa::Filters::Image::RegionGrow< _TImage, _TLabels, typename _TLabels::PixelType, CTBronchi::MoriLabellingTraits< _TImage, _TLabels > >
  38   {
  39   public:
  40     typedef CTBronchi::MoriLabellingTraits< _TImage, _TLabels > TTraits;
  41     fpaTraitsMacro( typename TTraits );
  42
  43     typedef fpa::Filters::Image::RegionGrow< _TImage, _TLabels, TMark, TTraits > Superclass;
  44     typedef MoriLabelling Self;
  45     typedef itk::SmartPointer< Self > Pointer;
  46     typedef itk::SmartPointer< const Self > ConstPointer;
  47
  48     typedef fpa::Functors::RegionGrow::BinaryThreshold< TInputValue > TFunctor;
  49
  50   public:
  51     itkNewMacro( Self );
  52     itkTypeMacro( MoriLabelling, fpa::Filters::Image::RegionGrow );
  53
  54     itkGetConstMacro( VesselnessThreshold, double );
  55     itkSetMacro( VesselnessThreshold, double );
  56
  57     itkGetConstMacro( UpperThreshold, TInputValue );
  58     itkSetMacro( UpperThreshold, TInputValue );
  59
  60     ivqITKInputMacro( InputLabels, _TLabels );
  61     ivqITKInputMacro( InputVesselness, _TScalarImage );
  62
  63   protected:
  64     MoriLabelling( )
  65       : Superclass( ),
  66         m_VesselnessThreshold( 5 ),
  67         m_UpperThreshold( -650 )
  68       {
  69         ivqITKInputConfigureMacro( InputLabels, _TLabels );
  70         ivqITKInputConfigureMacro( InputVesselness, _TScalarImage );
  71         this->m_Functor = TFunctor::New( );
  72         this->SetPredicate( this->m_Functor );
  73       }
  74
  75     virtual ~MoriLabelling( )
  76       {
  77       }
  78
  79     virtual const itk::DataObject* _GetReferenceInput( ) const override
  80       {
  81         return( this->GetInputLabels( ) );
  82       }
  83     virtual void _BeforeGenerateData( ) override
  84       {
  85         this->Superclass::_BeforeGenerateData( );
  86
  87         this->m_Functor->SetUpperThreshold( this->m_UpperThreshold );
  88
  89         typedef itk::LabelStatisticsImageFilter< _TScalarImage, _TLabels > _TStats;
  90         typename _TStats::Pointer stats = _TStats::New( );
  91         stats->SetInput( this->GetInputVesselness( ) );
  92         stats->SetLabelInput( this->GetInputLabels( ) );
  93         stats->Update( );
  94
  95         typedef typename _TStats::ValidLabelValuesContainerType _TValidLbl;
  96         typedef typename _TStats::LabelPixelType                _TLabelPx;
  97         unsigned long minCount = std::numeric_limits< unsigned long >::max( );
  98         double vAvg = 0, vStd = 0;
  99         typename _TValidLbl::const_iterator vIt = stats->GetValidLabelValues( ).begin( );
 100         for( ; vIt != stats->GetValidLabelValues( ).end( ); ++vIt )
 101         {
 102           if( stats->HasLabel( *vIt ) )
 103           {
 104             unsigned long c = stats->GetCount( *vIt );
 105             if( c < minCount )
 106             {
 107               minCount = c;
 108               vAvg = stats->GetMean( *vIt );
 109               vStd = stats->GetSigma( *vIt );
 110
 111             } // fi
 112
 113           } // fi
 114
 115         } // rof
 116         this->m_MinVesselness = vAvg + ( vStd * this->m_VesselnessThreshold );
 117       }
 118
 119     virtual void _PostComputeOutputValue( TNode& n ) override
 120       {
 121         this->Superclass::_PostComputeOutputValue( n );
 122         if( n.Value == this->GetInsideValue( ) )
 123         {
 124           const _TLabels* labels = this->GetInputLabels( );
 125           const _TScalarImage* vesselness = this->GetInputVesselness( );
 126           if( labels->GetPixel( n.Vertex ) == 0 )
 127           {
 128             if( this->m_MinVesselness < vesselness->GetPixel( n.Vertex ) )
 129               n.Value = this->GetInsideValue( );
 130             else
 131               n.Value = 0;
 132
 133           } // fi
 134
 135         } // fi
 136       }
 137
 138   private:
 139     // Purposely not implemented.
 140     MoriLabelling( const Self& other );
 141     Self& operator=( const Self& other );
 142
 143   protected:
 144     typename TFunctor::Pointer m_Functor;
 145     double m_VesselnessThreshold;
 146     double m_MinVesselness;
 147     TInputValue m_UpperThreshold;
 148   };
 149
 150 } // ecapseman
 151
 152 #endif // __CTBronchi__Functions__h__
 153
 154 // eof - $RCSfile$